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Cigarette smoking is known to elevate risk for neuropsychiatric conditions such as depression and dementia. We found that smoking was associated with smaller total gray and white matter volume, increased white matter lesions, and variation in specific gray matter regions and white matter tracts. By controlling for important variables that often co-occur with smoking, such as alcohol use, this study identified distinct associations between smoking and brain structure, highlighting potential mechanisms of risk for common neuropsychiatric consequences of smoking such as depression and dementia.